They've both dominated in different ways. Phelps has won more medals, but the way in which Bolt won the 100m and 200m race was incredible IMO. He just made the rest of the sprinters look pedestrian. He completely embarrassed them. You could argue that Phelps did that in a few of his races, but he didn't have the same effect, compared to when Bolt won the 100m. Im going to go for Bolt just for his charisma.

Bolt, based on the idea that running is perhaps the most accessible sport to the world's population (whereas swimming isn't) and the completely illogical nature of all swimming events except freestyle. To take nothing away from Phelps though, still an astonishing achievement.